I’m trying to test a thresholding method I’ve developed and I want to validate what I see in MATLAB with what I should see in CellProfiler. What is the constant by which I can convert intensities that range from 0 to 65536 (16 bit) in MATLAB, to 0 to 1 in CellProfiler. For example is I know the pixel intensity in MATLAB equals 10000, what does that value equal in the scale CellProfiler uses? I know there is a rescaling module but if its possible I would like to know the rate to convert values.

Typically, you should divide by the bit depth maximum value, i.e. 2^16 for 16-bit images. Note that many cameras may be other than truly 16-bit (12-bit is common) however the file format bit depth may be greater (e.g. 16-bit). I said “typically” since if you have LoadImages’ “Rescale intensities?” checkbox checked, and the image’s metadata says the max possible intensity is something other than 2^16, then CP will scale to that value. Please see the Help below from LoadImages for the “Rescale intensities?” checkbox:

Does that make sense with what you are seeing in Matlab?
David